9RKV | pdb_00009rkv

Agrobacterium phage 7-7-1 tail fibers


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Insights into the structure and initial host attachment of the flagellotropic bacteriophage 7-7-1.

Noteborn, W.E.M.Ouyang, R.Hoeksma, T.Sidi Mabrouk, A.Esteves, N.C.Pelt, D.M.Scharf, B.E.Briegel, A.

(2025) Commun Biol 9: 55-55

  • DOI: https://doi.org/10.1038/s42003-025-09319-7
  • Primary Citation of Related Structures:  
    9HZ7, 9HZ8, 9RKQ, 9RKR, 9RKS, 9RKT, 9RKU, 9RKV

  • PubMed Abstract: 

    Understanding the structural and functional mechanisms of bacteriophage 7-7-1, the flagellotropic phage infecting Agrobacterium sp. H13-3, offers promising insights into phage-host interactions. Using single particle analysis (SPA) cryo-electron microscopy (cryo-EM), we determined the capsid, neck region, tail, and baseplate complex structures. Combined with cryo-electron tomography (cryo-ET) and machine learning methodologies, our findings indicate that phage 7-7-1 uses capsid fibers to establish initial contact with the host flagellum, followed by subsequent attachment to cell surface receptors. The study also demonstrated that capsid fibers are flexible and can interact with other phages and host flagella, suggesting a cooperative infection strategy. These results provide crucial structural insights and may open avenues for developing phage-based therapeutics against resistant bacterial pathogens.


  • Organizational Affiliation
    • Netherlands Centre for Electron Nanoscopy, Leiden University, Leiden, The Netherlands.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Structural proteinA,
B,
I [auth C],
J [auth D]
141Agrobacterium phage 7-7-1Mutation(s): 0 
UniProt
Find proteins for J7FAF8 (Agrobacterium phage 7-7-1)
Explore J7FAF8 
Go to UniProtKB:  J7FAF8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ7FAF8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Structural protein298Agrobacterium phage 7-7-1Mutation(s): 0 
UniProt
Find proteins for J7F9D4 (Agrobacterium phage 7-7-1)
Explore J7F9D4 
Go to UniProtKB:  J7F9D4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ7F9D4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Putative tail fiberK [auth M],
L [auth N],
M [auth O]
587Agrobacterium phage 7-7-1Mutation(s): 0 
UniProt
Find proteins for J7F8Z3 (Agrobacterium phage 7-7-1)
Explore J7F8Z3 
Go to UniProtKB:  J7F8Z3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ7F8Z3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)Netherlands184.034.014

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release
  • Version 1.1: 2025-12-17
    Changes: Data collection, Database references
  • Version 1.2: 2026-01-21
    Changes: Data collection, Database references